How to include samples names in assignTaxonomy of DADA2

Question

[sankadinesh]

Dear All, I gave carried out assignTaxonomy for 3 samples using the following command. I would like to know how to include sample names to the resultant file.

taxa <- assignTaxonomy(seqtab.nochim, 
                       "/Users/apple/Desktop/Databases/dada/dada.good.fasta", 
                       multithread=TRUE)

Regards, Dinesh S L

Answer 1

[antonioggsousa]

Hi,

You cannot do it. The taxa object is a taxonomy table that maps the ASVs (Amplicon Sequence Variants) to the respective taxonomy, where each column represents a different taxonomic rank, and each row represents a different ASV. So, no samples here.

What probably you're interested in is how to combine the taxonomy table with the ASV count table (with samples on the rows and the ASVs on the columns) built before. But that is another question, and it depends on your data structure etc.

If you want to analyze this data downstream on phyloseq, there is no need, because dada2 tutorial provides you a description how to do it: https://benjjneb.github.io/dada2/tutorial.html

I hope this helps,

António